I am a computational evolutionary biologist interested in identifying ecologically and clinically important signatures of positive natural selection in microbial genomes. My basic approach can be described as 'reverse ecology,' where patterns of variation in microbial genomes are analyzed to learn about the underlying ecology of wild populations.

Graduate students / Étudiants gradués

Inès LevadeResearch interests: Cholera is a severe, waterborne diarrheal disease that affects millions of people each year. Recent advances in bacterial genomics have rapidly altered our understanding of the macroevolution of Vibrio cholerae, the causative agent of this disease, but little is known about its short-term evolution, within households and within individuals. The goal of my research is to characterize V. cholerae genomic diversity at a spatial and temporal scale relevant to micro-epidemics, following a population genomic approach that can provide insights into the transmission and adaptation of this pathogen.

Previous research: I received my B.S. in Biochemistry and my M.S. in Anthropobiology from the Université Paul Sabatier in Toulouse, France. In March 2013, I joined the group of Ludovic Orlando, at the Centre for Geogenetics (Copenhagen, Denmark), on a 6 month internship where I worked on horse conservation genomics. I started my PhD at Université de Montréal and joined the Shapiro lab in January 2014.

Naíla Barbosa da CostaMicrobial communities can rapidly adapt to different environmental constraints but the evolutionary mechanisms of their differentiation are still not clear. During my PhD I intend to contribute to a better understanding of the ecological and evolutionary processes underlying the genetic differentiation in aquatic bacterial communities subjected to different chemical stressors, and also in cyanobacterial communities naturally exposed to phage that act as predators.​Previous research: I received my B.S. in Biology and my M.S. in Ecology from the Federal University of Minas Gerais, Brazil. As an undergrad I studied the cyanobacterial community diversity in saline alkaline lakes from the Pantanal wetland, and during my Masters I focused on molecular methods for detecting bloom-forming cyanobacteria in an urban reservoir.

Postdocs

Nicolas Tromas

Research interests: I am interested in the evolutionary biology of microbes. More concretely, I am especially interested in mechanisms that generate and maintain genetic variability, in dynamics of infection and more generally in host-pathogen interactions. Previous research: I did my PhD with Santiago F. Elena at the IBMCP (Instituto de Biologia Molecular y Celular de Plantas) of the Polytechnic University of Valencia, Spain. I used the plant virus TEV (Tobacco etch virus) as a model to address evolutionary questions. I estimated in vivo mutation and recombination rates, multiplicity and dynamics of infection during TEV infection in Nicotiana tabacum.

Research interests: I am currently working on structural variants and possible horizontal gene transfer events in Vibrio cholerae & enterotoxic strains of Escherichia coli.Previous research: My interest in genome plasticity began during my PhD, which was focused on mobile DNA in deep sea crustacean species (always keeping Barbara McClintock in mind!). Then I moved to the fascinating world of toxins in snakes and cone snails, before developing and applying metagenomic tools to study one of the most diverse and unknown habitats on earth (i.e soil).

Olga Pérez Carrascal

Research interests: I am interested in bacterial evolutionary genomics; how bacterial populations are organized in ecological and evolutionary units, and the extent of horizontal gene transfer and recombination within and among populations.Previous research: I received my M.S. in Biotechnology from the National University of Colombia and obtained my PhD in Biochemistry in the Center for Genomic Sciences at the National Autonomous University of Mexico (UNAM). During my PhD I worked on comparative and population genomic analysis of sympatric nitrogen-fixing rhizobia.

> Join the lab !

Applicants should have a strong background in microbiology, genomics, computational biology or evolutionary biology (or all of the above).

The lab has very limited funding for salaries, so applicants are expected to apply for external scholarships or fellowships, such as NSERC, FQRNT and CIHR. Some useful information for prospective students and postdocs from UdeM can be found here and at the UdeM Biology website.

Email Jesse to apply. Please include: - a description of your background and research interests- what you would like to work on in the lab- 3 references letters (need not be in your initial email, but will be required at some point)

​Lab alumni

​Catherine Girard (PhD, 2017): Now a postdoc with Alex Culley and Warwick Vincent at Université Laval​Larbi Bedrani (bioinformatics intern, summer-fall 2015): Now a postdoc at the University of Toronto, Mount Sinai Hospital, Department of Gastroenterology